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JAX BioConnect Query Command Line Tool

Access data and metadata from data packages

When computational research scientists or scientific software engineers work with BioConnect data sets, they should be able to they interrogate multidimensional data with access to the desciptive metadata right at hand. JBQ is the command line interface that provides users with access to BioConnect data packages directly from their terminal.

JAX scientists, bioinformaticians, and engineers can use JBQ to:

  • review ISA-formatted metadata,
  • filter datasets by relevant research characteristics,
  • identify tools in BioConnect relevant to a selected data set,
  • download datasets locally or on virtual servers (ex. HPC environment),
  • upload RO-Crates for derived datasets with new processes and workflows, ยง connect external systems (ex. glue) with BioConnect, and
  • share an RO-Crate with another researcher or engineer.

With these capabilities, we hope JBQ CLI will significantly reduce the friction surrounding JAX data analyses, exploration, and collaborative research.

Methods

From the command-line and within a folder where the JBQ_package is downloaded, you can use the methods listed below to interact with BioConnect.

login

  • Authenticate yourself as a valid JAX user and gain access to your unique user space.
  • Command: python3 jbq.py login

logout

  • Remove authentication from your machine to reduce risk of an illegitimate masquerader using your legitimate account.
  • Command: python3 jbq.py logout

explore

  • Review metadata of the RO-Crates in your user space with a text-user-interface (TUI).
  • Command: python3 jbq.py contents

focus

  • Reduce the list of RO-Crates in the TUI to a specific subset that share a particular research-relevant characteristic (ex. assays based on a specific tissue type).
  • Command: python3 jbq.py filter

mobilize

  • With a given RO-Crate selected in exploration mode, view the tools in BioConnect that may be relevant to analyzing or working with that data set.
  • Command: click within the TUI

deploy

  • Download an RO-Crate for use elsewhere.
  • Command: python3 jbq.py download

garrison

  • Having completed a transformation upon a previously deployed dataset, upload a derived-dataset into a new RO-Crate in BioConnect, identifying the lineage and ensuring reproducibility.
  • Command: python3 jbq.py upload
  • Variant: from within external systems (ex. glue) we may provide ways to directly repatriate your data into BioConnect through JBQ

share

  • Send an RO-Crate to an email address. Note: future versions may involve passing a link to JBQ that does not require JAX authentication for login.
  • Command: python3 jbq.py email